My patience is being sorely tested on this issue.

I have reported it every month since the game went live and it has remained unfixed.
Therefore, Cryptic cannot be ignorant of the problem

See screenshots:
Runabout Renaming Attempt 1
Runabout Renaming Attempt 2

As you can clearly see, the Runabout is indeed my active ship, so the error message appearing does not make sense.

This has been going on long enough, it's time to fix it!

You weren't supposed to be able to change the names of Runabouts originally, that functionality was added later. Ships purchased prior to the change cannot have their names changed in the traditional style. Try the command line function detailed here. That might work for you.

And If happy's suggestion doesn't work you can always dump your current runabout and get another, its not like they're very expensive to those that have been in the game a long time.

Nope, sadly it didn't work.

But thanks for telling me anyway.

To be honest, I don't want to waste credits on buying a ship I already purchased because Cryptic can't fix it.

I'll just keep reminding them and hope they get around to it eventually.